Summary of Study ST002513

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001620. The data can be accessed directly via it's Project DOI: 10.21228/M89B04 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002513
Study TitleGnotobiotic mice: Metabolites in serum of germ-free mice colonized with strains of gut bacterium Eggerthella lenta
Study TypeUntargeted LC-MS
Study SummaryThis dataset contains untargeted metabolomics analysis of serum of gnotobiotic mice either colonized with different strains of Eggerthella lenta for 2 weeks, or germ-free controls.
Institute
University of California, San Francisco
Last NameNoecker
First NameCecilia
Address513 Parnassus Ave HSW1501, San Francisco, CA 94143
Emailcecilia.noecker@ucsf.edu
Phone415-502-3264
Submit Date2023-03-21
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-04-10
Release Version1
Cecilia Noecker Cecilia Noecker
https://dx.doi.org/10.21228/M89B04
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001620
Project DOI:doi: 10.21228/M89B04
Project Title:Systems biology illuminates the alternative metabolic niche of the human gut bacterium Eggerthella lenta
Project Type:Untargeted LC-MS
Project Summary:Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem.
Institute:University of California, San Francisco
Department:Microbiology and Immunology
Laboratory:Peter Turnbaugh
Last Name:Noecker
First Name:Cecilia
Address:513 Parnassus Ave HSW1501, San Francisco, CA 94143
Email:cecilia.noecker@ucsf.edu
Phone:415-502-3264
Funding Source:This work was supported by the National Institutes of Health (2R01HL122593; 1R01AT011117; 1R01DK114034 to P.J.T., F32GM140808 to C.N.). P.J.T. is a Chan Zuckerberg Biohub Investigator and held an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund.
Publications:https://doi.org/10.1101/2022.09.19.508335
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